paleobuddy
paleobuddy can now simulate trait-dependent diversification, not just birth-death.
Comparison · Analytics
EvoPhylo vs qtl
A side-by-side editorial comparison of EvoPhylo and qtl — release velocity, themes, recent moves, and the top alternatives to consider.
EvoPhylo vs qtl: at a glance
What is EvoPhylo?
EvoPhylo added BEAST2 alongside MrBayes, then went quiet for two years.
EvoPhylo handles post-processing for Bayesian evolutionary rate and fossilized birth-death analyses, originally against MrBayes output. The 0.3.2 release added BEAST2 support for both FBD functions and rates analysis, making it usable by labs on either platform. Since then there has been one clock-partition fix and, in August 2025, a release whose notes say only that there are updated functions and bug fixes.
What is qtl?
R/qtl is in pure custodial mode: every recent release answers a compiler, not a user
R/qtl is the long-established R package for QTL mapping in experimental crosses, covering interval mapping, composite interval mapping, multiple-QTL model fitting and the associated cross data formats. Nothing in the recent release history adds capability. Version 1.74 removes an include that started warning on CRAN, 1.72 improves an error message in cim(), and 1.70 migrates the C code from Calloc/Realloc/Free to their R_-prefixed equivalents for R-devel.
EvoPhylo vs qtl: editorial side-by-side
EvoPhylo
0.0ANALYTICS
EvoPhylo added BEAST2 alongside MrBayes, then went quiet for two years.
◆ Current state
EvoPhylo handles post-processing for Bayesian evolutionary rate and fossilized birth-death analyses, originally against MrBayes output. The 0.3.2 release added BEAST2 support for both FBD functions and rates analysis, making it usable by labs on either platform. Since then there has been one clock-partition fix and, in August 2025, a release whose notes say only that there are updated functions and bug fixes.
◆ Where it's heading
The package's substantive arc ended with the 0.3.2 publication release, which arrived with peer-review revisions and three first-time contributors — the shape of software built to accompany a paper. What follows is thin: a MrBayes plotting correction in 0.3.3, then a two-year gap and a release with no described contents. The August 2025 entry may contain real work, but the notes give a reader nothing to judge.
◆ Prediction
Without release notes on the latest version there is no observable basis for predicting the next move; the two-year gap before it suggests activity tied to specific research needs rather than a maintenance cadence.
qtl
0.0ANALYTICS
R/qtl is in pure custodial mode: every recent release answers a compiler, not a user
◆ Current state
R/qtl is the long-established R package for QTL mapping in experimental crosses, covering interval mapping, composite interval mapping, multiple-QTL model fitting and the associated cross data formats. Nothing in the recent release history adds capability. Version 1.74 removes an include that started warning on CRAN, 1.72 improves an error message in cim(), and 1.70 migrates the C code from Calloc/Realloc/Free to their R_-prefixed equivalents for R-devel.
◆ Where it's heading
The package is being maintained, not developed. The work divides cleanly into keeping the compiled code building against successive R and toolchain versions, and fixing narrow bugs reported through the issue tracker. The C-level migrations in particular are compliance with R's tightening of its C interface rather than anything chosen. Users should read the stability as maturity: the analysis surface has been fixed for years and the maintainer is keeping it installable.
◆ Prediction
R has continued to restrict its non-API C entry points, and this package has already made two such migrations, so further compile-time compliance work is the most likely content of the next release.
Alternatives to EvoPhylo and qtl
Other Analytics products tracked by Sparkpulse, ranked by recent ship velocity. Each card links to a full editorial trajectory and lets you pivot into a head-to-head comparison with either EvoPhylo or qtl.
geodist
geodist stays dependency-free and fast, and warns you when 'cheap' distances stop being honest.
errors
errors keeps making uncertainty print the way each scientific field expects.
CMAQ
CMAQ went global in v5.5, and has been patching that surface ever since.
enpls
enpls has not changed its statistics since 2016 — only its website, twice.
grex
grex is a lookup table with a version number — it ships when the annotation moves.
See all EvoPhylo alternatives → · See all qtl alternatives →
Recent activity from EvoPhylo and qtl
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 8mo agoqtlRemove R_ext/PrtUtil.h include flagged by CRAN
- 8mo agoqtlClearer cim() error when multiple phenotypes are passed
- 11mo agoEvoPhyloEvoPhylo v. 0.3.5
- 1y agoqtlC memory calls migrated to R_Calloc/R_Realloc/R_Free
- 2y agoqtlFix Rprintf call and remaining compiler warnings
- 2y agoqtlFix summary.scanone() thresholds and csvs phenotype reading
- 3y agoEvoPhyloEvoPhylo 0.3.3 fixes back-rate plots for MrBayes
- 3y agoEvoPhyloEvoPhylo 0.3.2 adds BEAST2 support for FBD and rates
- 3y agoqtlFix addint()/addcovarint() with X chromosome QTL and missing phenotypes
Frequently asked questions
What is the difference between EvoPhylo and qtl?
They serve adjacent needs but don't currently overlap on shipped themes. EvoPhylo and qtl are shipping at a similar cadence (velocity 0.0 vs 0.0, both within Sparkpulse's "active" band). See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is EvoPhylo better than qtl?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. EvoPhylo and qtl are shipping at a similar cadence (velocity 0.0 vs 0.0, both within Sparkpulse's "active" band). For your specific use case, the alternatives sections above list other Analytics products to evaluate alongside.
What are the best alternatives to EvoPhylo?
Top EvoPhylo alternatives in Analytics are ranked by recent ship velocity. Browse the "EvoPhylo alternatives" section above for the current picks, or visit /alternatives/evophylo for the full list with editorial commentary on each.
What are the best alternatives to qtl?
Top qtl alternatives in Analytics are ranked by recent ship velocity. Browse the "qtl alternatives" section above for the current picks, or visit /alternatives/qtl-r for the full list with editorial commentary on each.